As a disclaimer before I start, I don't play many RTS games. I played Star Wars: Empire at War extensively, but only against the AI. I've played Heroes of Might and Magic III. I've tried Warhammer 40,000: Dawn of War, Starcraft, Achron, and a few Command and Conquer games. That's pretty much it. So this article won't be extremely long or in-depth.
But there's a reason for that. I like games with good stories, and as a genre, RTS games are terrible at telling stories.